BN1340 Genetic Spatial Mapping Report

Genetic Spatial Mapping Plot

This plot shows the spatial genetic mapping results across different tissues.

Cauchy Combination Result

This table presents the results of the Cauchy combination test, summarizing the genetic associations.

Annotation P Cauchy P Median
Layer 4 7.1011e-07 2.1238e-05
Layer 3 1.5754e-06 1.4863e-04
Layer 2 9.3449e-06 1.3773e-03
Layer 5 4.3020e-05 5.4817e-04
Layer 6 7.7244e-04 2.6783e-02
WM 9.9943e-01 2.6717e-01

Diagnosis Manhattan Plot

The Manhattan plot shows the association of SNPs with the top associated gene across the genome.

Gene Expression and GSS Distribution

Select a gene to view its expression distribution and gene specificity score (GSS).

Expression Distribution
SCN1B Expression Distribution
Gene Specificity Score (GSS)
SCN1B GSS Distribution

Top 50 Gene Diagnostic Info

This table lists the top 50 genes based on diagnostic criteria, including the gene specificity score (GSS) and PCC.

Gene Annotation Median GSS PCC
SCN1B Layer 4 3.6953 0.8277
INA Layer 4 3.5215 0.8229
NSG2 Layer 4 3.6689 0.8222
DIRAS1 Layer 4 3.2539 0.8180
KCNA2 Layer 4 3.4160 0.8136
VDAC3 Layer 4 3.0117 0.8124
RIMS3 Layer 4 3.1768 0.8111
CHGA Layer 4 3.4375 0.8111
VAMP1 Layer 4 3.7881 0.8110
AAK1 Layer 4 2.8994 0.8098
REEP2 Layer 3 2.6484 0.8093
TOLLIP Layer 4 3.3066 0.8077
AUXG01000058.1 Layer 4 3.2578 0.8077
NEFM Layer 3 3.7891 0.8072
GABRB2 Layer 4 3.3711 0.8066
INPP5F Layer 4 3.5137 0.8064
SPOCK2 Layer 4 3.0723 0.8056
ISCU Layer 4 3.0615 0.8056
NRXN1 Layer 4 3.3223 0.8054
NAP1L3 Layer 4 3.2285 0.8054
NSG1 Layer 3 3.1113 0.8054
CD99L2 Layer 4 2.8828 0.8052
TRIM37 Layer 4 3.3145 0.8048
CALY Layer 4 3.1562 0.8045
SNCG Layer 5 3.5137 0.8039
SYT13 Layer 4 2.8965 0.8036
CHD5 Layer 4 2.8145 0.8035
CAMK2G Layer 4 3.1660 0.8030
NAT8L Layer 3 3.2227 0.8029
CADM3 Layer 4 3.2119 0.8015
RAB6A Layer 4 2.9375 0.8013
SLC6A17 Layer 4 2.9248 0.8013
SLC12A5 Layer 4 3.4824 0.8011
OCIAD1 Layer 4 2.7939 0.8007
CPLX1 Layer 4 3.0889 0.8003
GABRD Layer 4 3.3291 0.7998
OAT Layer 4 2.9502 0.7990
GABRG2 Layer 4 3.2930 0.7986
GABRA1 Layer 4 3.3008 0.7972
YPEL5 Layer 4 3.3320 0.7970
NCS1 Layer 4 3.3145 0.7966
NAP1L5 Layer 4 3.3145 0.7964
GABBR2 Layer 4 2.8594 0.7958
CAMTA1 Layer 4 3.1973 0.7950
ATP2B2 Layer 4 3.4004 0.7944
KLHDC3 Layer 4 3.0918 0.7942
SCAMP5 Layer 4 3.0645 0.7939
KCNAB2 Layer 4 3.2969 0.7933
NDRG3 Layer 4 2.8740 0.7933
BTBD2 Layer 4 2.6777 0.7932

Running Info

Click to view detailed run information and parameters.

gsMap Version: 1.73.0

Parameters:

  • Sample Name: BN1340
  • Trait Name: PD
  • Summary Statistics File: /mnt/data/projects/ASAP/ST/gsMAP/GWAS_nallsEtAl2019_allSamples_allVariants.sumstats.gz
  • HDF5 Path: /mnt/data/projects/ASAP/ST/gsMAP/st_anndata_h5ads/st_adata_BN1340_for_gsmap.h5ad
  • Annotation: smoothed_label_s5
  • Spatial LDSC Save Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1340/spatial_ldsc
  • Cauchy Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1340/cauchy_combination
  • Report Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1340/report/PD
  • gsMap Report File: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1340/report/PD/BN1340_PD_gsMap_Report.html
  • Gene Diagnostic Info File: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1340/report/PD/BN1340_PD_Gene_Diagnostic_Info.csv
  • Report Generation Date: 2025-04-11 03:38:08
  • Number of Processes: 10
  • Spending Time: 0h 4m